Friday, October 29, 2010

China has officially built the world's faster computer. This is impressive. Most people have been saying that its all built from US parts. There is some truth to that. The CPUs and whatnot are nvidia GPUs and CPUs (AMD?) are US $tech.

However, the ever important interconnect is NOT American. This is homegrown and that is really impressive. Interconnects are hard. its also rumored to be twice as fast as QDR infiniband and laid out as a fat tree. its also rumored to use around 14 MW. That's excellent.

This has been compared to what the Japanese did with the Earth Simulator. That claimed the top spot for some time because it was around 4x+ faster than the US counterparts. The difference here between Tinhe-1A and the US counterparts is not that much, in comparison: 50%. I would expect this machine to be overtaken in a year at most. Possibly by June.

Congratulations to the Chinese. I wish I were going to SC10 now. Its sure to be an exciting event now. we'll see if the US can pull out any surprise benchmarks now. Never know. I doubt it though.

The giant dragonflies of ancient Earth with wingspans of up to 70 centimeters (28 inches) are generally attributed to higher oxygen atmospheric levels in the atmosphere in the past. New experiments in raising modern insects in various oxygen-enriched atmospheres have confirmed that dragonflies grow bigger with more oxygen, or hyperoxia.

However, not all insects were larger when oxygen was higher in the past. For instance, the largest cockroaches ever are skittering around today. The question becomes how and why do different groups respond to changes in atmospheric oxygen.

The secrets to why these changes happened may be in the hollow tracheal tubes insects use to breathe. Getting a better handle on those changes in modern insects could make it possible to use fossilized insects as proxies for ancient oxygen levels.

"Our main interest is in how paleo-oxygen levels would have influenced the evolution of insects," said John VandenBrooks of Arizona State University in Tempe. To do that they decided to look at the plasticity of modern insects raised in different oxygen concentrations. The team raised cockroaches, dragonflies, grasshoppers, meal worms, beetles and other insects in atmospheres containing different amounts of oxygen to see if there were any effects.

One result was that dragonflies grew faster into bigger adults in hyperoxia. However, cockroaches grew slower and did not become larger adults. In all, ten out of twelve kinds of insects studied decreased in size in lower oxygen atmospheres. But there were varied responses when they were placed into an enriched oxygen atmosphere. VandenBrooks will be presenting the results of the work on Monday, Nov. 1 at the annual meeting of the Geological Society of America in Denver.

"The dragonflies were the most challenging of the insects to raise," said VandenBrooks because, among other things, there is no such thing as dragonfly chow. As juveniles they need to hunt live prey and in fact undergraduate students Elyse Muñoz and Michael Weed working with Dr. VandenBrooks had to resort to hand feeding the dragonflies daily.

"Dragonflies are notoriously difficult to rear," said VandenBrooks. "We are one of the only groups to successfully rear them to adulthood under laboratory conditions."

Once they had worked that out, however, they raised three sets of 75 dragonflies in atmospheres containing 12 percent (the lowest oxygen has been in the past), 21 percent (like modern Earth's atmosphere) and 31 percent oxygen (the highest oxygen has been).

Cockroaches, as anyone who has fought them at home knows, are much easier to rear. That enabled the researchers to raise seven groups of 100 roaches in seven different atmospheres ranging from 12 percent to 40 percent oxygen mimicking the range of paleo-oxygen levels. Cockroaches took about twice as long to develop in high oxygen levels.

"It is the exact opposite of what we expected," said VandenBrooks. One possibility is that the hyperoxic reared roaches stayed in their larval stage longer, perhaps waiting for their environment to change to a lower, maybe less stressful oxygen level.

This surprising result prompted the researchers to take a closer look at the breathing apparatus of roaches – their tracheal tubes. These are essentially hollow tubes in an insect's body that allow gaseous oxygen to enter directly into the insect tissues.

VandenBrooks and his team took their hyperoxic reared roaches to Argonne National Lab's x-ray synchrontron imaging facility to get a closer look at the tracheal tubes. The x-ray synchrontron is particularly good at resolving the edges where things of different phases meet – like solids on liquids or gas on solids. That's just what the inside of a tracheal tube is.

What they found was that the tracheal tubes of hyperoxic reared roaches were smaller than those in lower oxygen atmospheres. That decrease in tube size with no increase in the overall body size would allow the roaches to possibly invest more in tissues used for other vital functions other than breathing – like eating or reproducing. The roaches reared in hypoxia (lower oxygen) would have to trade off their investment in these other tissues in order to breathe.

The next step, said VandenBrooks, will be to look closely at the tracheal tubes of insects fossilized in amber to see what they might say about oxygen levels at various times in the past. These might possibly serve as a proxy for paleo-oxygen levels.

More than two and a half billion years ago, Earth differed greatly from our modern environment, specifically in respect to the composition of gases in the atmosphere and the nature of the life forms inhabiting its surface. While today's atmosphere consists of about 21 percent oxygen, the ancient atmosphere contained almost no oxygen. Life was limited to unicellular organisms. The complex eukaryotic life we are familiar with – animals, including humans – was not possible in an environment devoid of oxygen.

The life-supporting atmosphere Earth's inhabitants currently enjoy did not develop overnight. On the most basic level, biological activity in the ocean has shaped the oxygen concentrations in the atmosphere over the last few billion years. In a paper published today by Nature Geoscience online, Arizona State University researchers Brian Kendall and Ariel Anbar, together with colleagues at other institutions, show that "oxygen oases" in the surface ocean were sites of significant oxygen production long before the breathing gas began to accumulate in the atmosphere.

By the close of this period, Earth witnessed the emergence of microbes known as cyanobacteria. These organisms captured sunlight to produce energy. In the process, they altered Earth's atmosphere through the production of oxygen – a waste product to them, but essential to later life. This oxygen entered into the seawater, and from there some of it escaped into the atmosphere.

"Our research shows that oxygen accumulation on Earth first began to occur in surface ocean regions near the continents where the nutrient supply would have been the highest," explains Kendall, a postdoctoral research associate at the School of Earth and Space Exploration in ASU's College of Liberal Arts and Sciences. "The evidence suggests that oxygen production in the oceans was vigorous in some locations at least 100 million years before it accumulated in the atmosphere. Photosynthetic production of oxygen by cyanobacteria is the simplest explanation."

The idea of "oxygen oases," or regions of initial oxygen accumulation in the surface ocean, was hypothesized decades ago. However, it is only in the past few years that compelling geochemical evidence has been presented for the presence of dissolved oxygen in the surface ocean 2.5 billion years ago, prior to the first major accumulation of oxygen in the atmosphere (known as the Great Oxidation Event).

Kendall's work is the latest in a series of recent studies by a collaborative team of researchers from ASU; University of California, Riverside; and University of Maryland that point to the early rise of oxygen in the oceans. Together with colleagues from University of Washington and University of Alberta, this team first presented evidence for the presence of dissolved oxygen in these oceans in a series of four Science papers over the past few years. These papers focused on a geologic formation called the Mt. McRae Shale from Western Australia. One of these papers, led by the ASU team, presented geochemical profiles that showed an abundance of two redox-sensitive elements – rhenium (Re) and molybdenum (Mo) – implying that small amounts of oxygen mobilized these metals from the crust on land or in the ocean, and transport them through an oxic surface ocean to deeper anoxic waters where the metals were hidden into organic-rich sediments. Kendall participated in this research while a postdoctoral student at the University of Alberta.

Kendall's goal in the new project was to look for evidence of dissolved oxygen in another location. He wanted to see if the geochemical evidence from the Mt. McRae Shale in Western Australia would be found in similarly-aged rocks from South Africa. Those rocks were obtained in a project supported by the Agouron Institute. Kendall's research was supported by grants from NASA and the National Science Foundation.

What Kendall discovered was a unique relationship of high rhenium and low molybdenum enrichments in the samples from South Africa, pointing to the presence of dissolved oxygen on the seafloor itself.

"In South Africa, samples from the continental slope beneath the shallower platform were thought to be deposited at water depths too deep for photosynthesis. So it was a big surprise that we found evidence of dissolved oxygen on the seafloor at these depths. This discovery suggests that oxygen was produced at the surface in large enough quantities that some oxygen survived as it was mixed to greater depths. That implies a significantly larger amount of oxygen production and accumulation in 'oxygen oases' than was previously realized."

A key contribution to this study came from Christopher Reinhard and Timothy Lyons, collaborators at the University of California, Riverside, and Simon Poulton at Newcastle University, who found that the chemistry of iron (Fe) in the same shales is also consistent with the presence of dissolved oxygen.

"It was especially satisfying to see two different geochemical methods – rhenium and molybdenum abundances and Fe chemistry – independently tell the same story," Kendall noted.

Evidence that the atmosphere contained at most minute amounts of oxygen came from measurements of the relative abundances of sulfur (S) isotopes. These measurements were performed by Alan Kaufman, a collaborator at the University of Maryland.

New research from the Centre for Addiction and Mental Health (CAMH) and The Hospital for Sick Children (SickKids), both in Toronto, Canada provides further clues as to why Autism Spectrum Disorder (ASD) affects four times more males than females. The scientists discovered that males who carry specific alterations of DNA on the sole X-chromosome they carry are at high risk of developing ASD. The research is published in the September 15 issue of Science Translational Medicine.

ASD is a neurological disorder that affects brain functioning, resulting in challenges with communication and social interaction, unusual patterns of behaviour, and often, intellectual deficits. ASD affects one in every 120 children and a startling one in 70 boys. Though all of the causes of ASD are not yet known, research has increasingly pointed towards genetic factors,. In recent years, several genes involved in ASD have successfully been identified.

The research team was led by Dr. John B. Vincent, Senior Scientist and head of CAMH's Molecular Neuropsychiatry and Development Laboratory and Dr. Stephen Scherer, Senior Scientist and Director of The Centre for Applied Genomics at SickKids, and Director of the McLaughlin Centre at the University of Toronto. The scientists analyzed the gene sequences of 2,000 individuals with ASD, along with others with an intellectual disability, and compared the results to thousands of population controls. They found that about one per cent of boys with ASD had mutations in the PTCHD1 gene on the X-chromosome. Similar mutations were not found in thousands of male controls. Also, sisters carrying the same mutation are seemingly unaffected.

"We believe that the PTCHD1 gene has a role in a neurobiological pathway that delivers information to cells during brain development – this specific mutation may disrupt crucial developmental processes, contributing to the onset of autism." said Dr. Vincent. "Our discovery will facilitate early detection, which will, in turn, increase the likelihood of successful interventions."

"The male gender bias in autism has intrigued us for years and now we have an indicator that starts to explain why this may be," says Dr. Scherer. "Boys are boys because they inherit one X-chromosome from their mother and one Y-chromosome from their father. If a boy's X-chromosome is missing the PTCHD1 gene or other nearby DNA sequences, they will be at high risk of developing ASD or intellectual disability. Girls are different in that, even if they are missing one PTCHD1 gene, by nature they always carry a second X-chromosome, shielding them from ASD." Scherer adds, "While these women are protected, autism could appear in future generations of boys in their families."

There was a relatively recent study that found that autism was more common in affluent caucasian families with older parents. It went rather contrary to the environmental causes hypothesis. If I have time (HA!) I'll find and put a link to that one.

It makes me wonder if this can be directly linked to postponing having kids: we already know of increased rates of other issues such as down's and whatnot. Perhaps the damage is being caused by meiosis potentially going slightly off tracks in (some) older women. As more women postpone their fertility, the number of autistic children rises and will continue to do for generations afterwards because their daughters might be carriers of the damaged regions on their inherited X chromosomes.

I can't imagine that this will be a popular study result or my hypothesis either.

A team of scientists, led by biogeochemists at the University of California, Riverside, has found new evidence linking "Snowball Earth" glacial events to the rise of early animals.

The controversial Snowball Earth hypothesis posits that the Earth was covered from pole to pole by a thick sheet of ice lasting, on several occasions, for millions of years. These glaciations, the most severe in Earth history, occurred from 750 to 580 million years ago. The researchers argue that the oceans in the aftermath of these events were rich in phosphorus, a nutrient that controls the abundance of life in the oceans.

The UC Riverside team and colleagues tracked phosphorus concentrations through Earth's history by analyzing the composition of iron-rich chemical precipitates that accumulated on the seafloor and scavenged phosphorus from seawater. Their analyses revealed that there was a pronounced spike in marine phosphorus levels in the mid-Neoproterozoic (from ~750 to ~635 million years ago).

To explain these anomalously high concentrations, the researchers argue that the increase in erosion and chemical weathering on land that accompanied Snowball Earth glacial events led to the high amounts phosphorus in the ocean. The abundance of this nutrient, which is essential for life, in turn, led to a spike in oxygen production via photosynthesis and its accumulation in the atmosphere, facilitating the emergence of complex life on Earth.

Study results appear in the Oct. 28 issue of Nature.

"In the geological record, we found a signature for high marine phosphorus concentrations appearing in the immediate aftermath of the Snowball Earth glacial events," said Noah Planavsky, the first author of the research paper and a graduate student in the Department of Earth Sciences. "Phosphorus ultimately limits net primary productivity on geological timescales. Therefore, high marine phosphorus levels would have facilitated a shift to a more oxygen-rich ocean-atmosphere system. This shift could have paved the way for the rise of animals and their ecological diversification. Our work provides a mechanistic link between extensive Neoproterozoic glaciations and early animal evolution."

Planavsky explained the link between marine phosphorus concentrations and the levels of oxygen in the atmosphere.

"High phosphorus levels would have increased biological productivity in the ocean and the associated production of oxygen by photosynthesis," he said. "Much of this organic matter is consumed, in turn, as a result of respiration reactions that also consume oxygen. However, the burial of some proportion of the organic matter results in a net increase of oxygen levels in the atmosphere."

Until now, scientists believed that geochemical conditions in the iron-rich ocean would have led to low phosphorus concentrations. The UC Riverside researchers found no evidence of a phosphorus crisis after Snowball Earth glacial events, however, finding instead indications of an abundance of phosphorus.

Scientists have discovered in China the first complete skeleton of a pivotal ancestor of Earth's largest land animals – the sauropod dinosaurs. The new species, tentatively dubbed Yizhousaurus sunae, lived on the flood plains around Lufeng in the Yunnan Province of South China about 200 million years ago. The species helps explain how the iconic four-footed, long-necked sauropod dinosaurs evolved.

Unlike the 120-foot-long, 100-ton sauropod giants that came later, Yizhousaurus was about 30 feet in length, but it shows all of the hallmarks of later sauropods: the beginning of a long neck, a robust skeleton and four-legged posture. It also comes with an intact fossilized skull – which is very rare and crucial for understanding its place in the evolution of sauropods.

"Sauropods have these big bones but their skulls are very lightly constructed and also very small," said paleontologist Sankar Chatterjee of Texas Tech University. Chatterjee presents the discovery on Sunday, Oct. 31 at the annual meeting of the Geological Society of America in Denver.

Yizhousaurus's skull is broad, high and domed, less than a foot long with a short snout, eye sockets on the sides for scanning enemies. It has an unusually wide and U-shaped jaw, in top view, like that seen in later Camarasaurus, said Chatterjee. Numerous serrated and spoon-shaped teeth of the upper and lower jaws would shear and slide past each other for cutting plant material during feeding. The sturdy teeth and raised neck let the animal very easily nip small branches from treetops and then chew the plant material.

Wednesday, October 06, 2010

The oldest evidence of the dinosaur lineage—fossilized tracks—is described this week in Proceedings of the Royal Society B. Just one or two million years after the massive Permian-Triassic extinction, an animal smaller than a house cat walked across fine mud in what is now Poland. This fossilized trackway places the very closest relatives of dinosaurs on Earth about 250 million years ago—5 to 9 million years earlier than previously described fossilized skeletal material has indicated. The paper also described the 246-million-year-old Sphingopus footprints, the oldest evidence of a bipedal and large-bodied dinosaur.

"We see the closest dinosaur cousins immediately after the worst mass extinction," says Stephen Brusatte, a graduate student affiliated with the Division of Paleontology at the American Museum of Natural History. "The biggest crisis in the history of life also created one of the greatest opportunities in the history of life by emptying the landscape and making it possible for dinosaurs to evolve."

The new paper analyzes three sets of footprints from three different sites in the Holy Cross Mountains of central Poland. The sites, all quarries within a 25-mile radius of each other, are windows into three ecosystems because they represent different times periods. The Stryczowice trackway is the oldest at 250 million years. The Baranów trackway is the most recent at 246 million years of age while the Wióry trackway is sandwiched in time between the others.

Because footprints are only an imprint of a small part of the skeleton, identification of trackmakers is often tricky. Luckily, dinosaurs have a very distinctive gait, especially when compared to their diapsid relatives (the evolutionary group that includes birds, reptiles, and extinct lineages) like crocodiles and lizards. While lizards and crocodiles have a splayed walking style, dinosaurs place their two feet closer together. The footprints at all three Polish sites show this feature as well as indisputable dinosaur-like features, including three prominent central toes and reduced outer two toes, a parallel alignment of these three digits (a bunched foot), and a straight back edge of footprints, additional evidence of a dinosaur-like simple hinged ankle.

Because all of these features are seen in footprints at the oldest site, Brusatte and colleagues conclude that the Stryczowice prints—which are only a few centimeters in length—are the oldest evidence of the dinosaur lineage. These dinosaurs, though, are considered "stem dinosaurs," or the immediate relatives of dinosaurs not part of the slightly more derived clade that technically defines dinosaurs. Also, this animal did walk on all four limbs, an abnormal posture for early dinosaurs and their close relatives, although it appears that its forelimbs were already being reduced to more dinosaur-like proportions since the footprints overstep handprints.

The Baranów and Wióry trackways show changes early in the evolutionary history of dinosaurs. Wióry at 248 million years ago shows slight diversification in the types of tracks, but all tracks remain quadrupedal. Footprints from Baranów at 246 million years ago, however, may be the earliest evidence of moderately large-bodied and bipedal true dinosaurs. These tracks, which are called Sphingopus, are 15 centimeters long.